Hi,
For adding a character, i doubt anyone have done this before (and i don't know if it's really possible).
But, to change one character by another, if you search on gbatemp, you will find things like this:
Two try:
http://gbatemp.net/threads/editing-players-and-their-moveset-on-inazuma-eleven-2-blizzard-e.333140/
http://gbatemp.net/threads/help-inazuma-eleven-2-character-hack.338622/
You can find in these a tool from roxas to do that (but i don't know if it could be used on IE3).
TyraNtM has allready insert Layton characters in his hack to IE2. So it's possible, and the format for characters in IE2 is nearly the same with those in IE3 (but different). I think TyraNtM has used the Roxas tool to do it, but maybe it's not like that.
http://gbatemp.net/threads/inazuma-eleven-2-blizzard-remastered-version.324476/
And probably a way to change it is to use Tinke (and you can improve it if you have some coding skills):
http://gbatemp.net/threads/tinke-0-7-2.303529/
So, you have to study how the tool work on IE2, change some characters, and after, try it on IE3 and modify what it must be done to do the work.
EDIT:
I don't know if I have rights to post here a link to another forum, but it could be useful to respond the question. (moderator, suppress my link if it's not allowed here)
You have a team that have work on extracting each character in IE3.
Maybe you could start your search with that:
The Ogre Headshots Ripping Project
http://www.spriters-resource.com/community/showthread.php?tid=19289
They have only extracted 2D sprites, so, for the 3D model, you have to study the IE2 hack from TyraNtM.